博碩士論文 103223023 詳細資訊




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姓名 沈?全(Po-Chuan Shen)  查詢紙本館藏   畢業系所 化學學系
論文名稱
(Improvement of Calcium and Magnesium Cation-Anion Interaction Force Fields for Electrolyte Simulations)
檔案 [Endnote RIS 格式]    [Bibtex 格式]    至系統瀏覽論文 (2018-3-1以後開放)
摘要(中) 水溶劑中的離子和離子對的幾何結構、分子動態和水合能是一個長期引人注目的主題,且已經受到許多不同的實驗的以及理論的方法研究。特別是金屬離子中中的鈣離子和鎂離子在細胞的生物功能中為必要的離子。先前的研究已經指出在使用經驗力場的分子動態模擬中觀察到濃度高的電解質溶液有過量的離子簇形成;這個結果會導致不準確的離子與水的配位數。此方式可能會導致在高負電荷密度的生物系統,例如DNA/RNA和磷脂質有不準確的配位。由於不適當的陽離子和陰離子的蘭納-瓊斯作用參數可能會導致上述的問題,其一般在分子動態模擬中是運用Lorentz-Berthelot combining rule來逼近。
在本次實驗中我們先由在大範圍濃度實驗的配位數為基準來測試Lim和Roux的鈣離子和鎂離子參數。Lim的鈣離子參數可以良好的在低濃度下再現出實驗的配位數,但是在高濃度下會有大量的離子對生成。我們最佳化Ca2+-Cl- 和 Mg2+-Cl-的蘭納-瓊斯作用參數使其在高濃度下仍可以再現出實驗的配位數。有趣的是我們最佳化的Ca2+-Cl- 和 Mg2+-Cl-的蘭納-瓊斯作用參數可以在大範圍濃度下再現出實驗的配位數。此外我們有詳細的分析1M氯化鈣溶液結構、動態和自由能。
摘要(英) Geometry, molecular dynamics, and hydration energies of ions and ion-pairs in aqueous solution have long been an attractive topic under investigated in terms of various experimental, theoretical, and simulation methods. Particularly, calcium (Ca2+) and magnesium (Mg2+) play significant roles for biochemical functions of cells. Previous studies have shown that classical molecular dynamics simulations using empirical force field observed excess ion cluster formation in concentrated electrolyte solutions leading to incorrect coordination numbers of ions with water molecules. These artifacts might lead to inaccurate coordination of cations with high-density negatively charged biomolecular systems such as phospholipids and DNA/RNA. The above mentioned problem might be due to improper cation-anion Lennard-Jones interacting parameters, approximated by Lorentz-Berthelot combining rule, which are generally default used in MD simulations.
In this study, we first test the performance of Lim’s parameters1 and Roux’ parameters2 of Ca2+ and Mg2+ cations based on their experimental coordination number for a wide range of salt concentration. Lim’s parameters1 of Ca2+ cation can well reproduce the coordination number at low slat concentration while have significant ion-pair formation at higher salt concentrations. We optimized the Ca2+-Cl- and Mg2+-Cl- interacting L-J parameters to reproduce the experimental measured coordination number at high salt concentration. Interestingly, our optimized Ca2+-Cl- and Mg2+-Cl- interacting L-J parameters well reproduce the coordination numbers for a wide range of salt concentration. Moreover, we analyzed the structure, dynamics, and free energy profile of 1 M CaCl2 solution in details.
關鍵字(中) ★ 氯化鈣溶液
★ 離子對
★ 配位數
★ 蘭納-瓊斯勢
關鍵字(英)
論文目次 摘要...................................................... I
Abstract ................................................ II
Contents ............................................... III
List of Figures ......................................... IV
List of Tables .......................................... VI
Chapter 1 - Introduction ................................. 1
Chapter 2 - Computational Methods .........................8
Chapter 3 - Results and Discussion ...................... 10
3.1 Calculated Coordination Numbers and Ion Pairs ....... 10
3.2 Improvement of Cation-Anion Interaction Parameters .. 17
3.3 Structures, Dynamics, and Free Energies of CaCl2 Solution .................... 29
Chapter 4 - Conclusions and Summary ..................... 49
Acknowledgments ..........................................50
Reference ............................................... 51
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指導教授 蔡惠旭 審核日期 2017-2-17
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